In the default Debian desktop (Gnome, I believe, definitely not KDE) I have lost the ability to open the "system settings" item in either the Applications/System Tools/Preferences menu or the dropdown menu from the username in the upper right corner.
This was triggered by my installation of a new video card. I suspect the installation of the Radeon Catalyst control panel, which allows you to control the video card settings, is the exact point it happened. Can anybody verify if fglrx-control disables system settings? I believe that is the only package I chose manually, the rest came along with fglrx.